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Freeman, Dennis, Martha Gray, and Alexander Aranyosi, HST.410J Projects in Microscale Engineering for the Life Sciences, Spring 2007. (Massachusetts Institute of Technology: MIT OpenCourseWare), (Accessed 09 Jul, 2010). License: Creative Commons BY-NC-SA

Projects in Microscale Engineering for the Life Sciences

Spring 2007

People in cleanroom suits view magnified wafer pattern on screen.
Members of the class inspect one of the wafers they created in lab. (Image by A. Aranyosi.)

Course Description

This course is a project-based introduction to manipulating and characterizing cells and biological molecules using microfabricated tools. It is designed for first year undergraduate students. In the first half of the term, students perform laboratory exercises designed to introduce (1) the design, manufacture, and use of microfluidic channels, (2) techniques for sorting and manipulating cells and biomolecules, and (3) making quantitative measurements using optical detection and fluorescent labeling. In the second half of the term, students work in small groups to design and test a microfluidic device to solve a real-world problem of their choosing. Includes exercises in written and oral communication and team building.

Special Features

  • Image gallery

Technical Requirements

Special software is required to use some of the files in this course: .m.


Contents - Engineering Systems at the Scale of Cells and Biomolecules

  • How do you build tools that can manipulate cells?
    • Lithography: Shrinking patterns to the micro-scale
    • Soft lithography: Making bio-compatible fluid reservoirs
    • Rapid prototyping: Using existing microscale structures to test new ideas
  • How do you measure properties of individual cells?
    • Optical imaging
    • Electrical signals
    • Cell sorting
    • Averaging

Teaching/Learning Activities

  • Two lectures each week to introduce new material.
  • Two lab sessions each week to provide hands-on experience.
  • One project to help students learn to pose testable hypotheses, to conduct research, and to communicate results.
  • Weekly homework assignments to encourage students to actively assimilate the course material.


Weekly homework assignments provide an opportunity to develop intuition for new concepts by actively applying the new concepts to solve problems and answer questions. The process of actively struggling with the use of new ideas until you understand them is an effective and rewarding form of education.

Weekly homework assignments will be distributed in class on Thursdays and will be due the following Thursday at the start of lecture. Late homework will not be accepted. Homework assignments will be corrected, graded, and returned the week after they are due. The solution to each homework assignment will generally be made available to the class a few days after the homework due date. Paper copies of homework assignments and solutions will not be distributed.

Homework problems will be chosen for their educational value. Reading someone's solution to a problem is not educationally equivalent to generating your own solution. If you skip the process of personally struggling with the use of new concepts, you will have destroyed your most important educational experience.

Collaboration Policy

We encourage students to discuss the homework with other students and with the teaching staff to better understand the concepts. However, we expect that you wrote the solutions that you submit under your name. Students should not use solutions of other students (from this year or from previous years) in preparing their own solutions. Students should not take credit for computer code or electronic plots generated by other students. Students should not share their solutions with other students. Any student caught plagiarizing will receive a grade of zero on the assignment. All incidents of plagiarism will be reported to the Committee on Discipline (COD). More information about what constitutes plagiarism can be found at MIT Academic Integrity.


This subject includes one project. In this project, students are asked to improve on an existing microfluidic design or technique. Students will be expected to demonstrate the improvement with a working prototype. The project provides an opportunity to learn about, planning R&D and experiments, acquiring, processing, and interpreting data, communicating the results to others. The project requires a written proposal, which includes a well-defined hypothesis and procedures to test the hypothesis. Students are encouraged to work in pairs for the project. Partners are encouraged to submit a joint proposal and to cooperate in design, in collecting and processing data, in discussing interpretations, and in preparing their reports. Partners are also encouraged to submit a joint report. We strongly believe that students learn more by working with other students than by working in isolation. The final report will be presented in the form of a short talk to the class. It should be 12 minutes in length and should be delivered during the next to last week of the semester. The report has a firm due date, which is listed on the subject calendar. There are severe lateness penalties for missing the due date.

Communications Intensive

This subject is communications intensive. We feel that communications skills are essential for professional engineers and scientists. We also feel that the process of creating written manuscripts and oral presentations can help clarify thinking and can be an effective way to learn technical material. Homework assignments will often ask you to explain something or to define something that you have been taught. In addition the project is communications intensive. For the project, you and your partner must submit a written proposal and revise the proposal until it is approved by the staff. You and your partner must prepare a formal report that is structured as a scientific oral presentation. First drafts of the report are due approximately one week before the final draft, and will be reviewed by the technical staff, staff from the Writing Program, and by student peers. You and your partner will be assigned to prepare a written critique of a first draft from a different team. The critiques will be discussed during a special session held between the first draft and final draft deadlines. Students can satisfy their freshman year communications requirement by taking this subject.


Because of the project-oriented nature of this subject, grades will depend strongly on the final project. It should be noted that this project grade itself has several components which will be graded separately (e.g., proposal, first draft, written critique, etc.). In addition, your final presentation will be graded on several metrics (technical content, effective use of slides, clarity of presentation, etc.). More detail on grading is provided in the assignments section of this site. The weighting factors for determining letter grades are:

Homework 50%
Lab project 50%

For students near grade boundaries, other factors may be taken into account, including participation in class, laboratory performance not evidenced in the laboratory grade, etc. The grades are determined by the staff.


The course has no required text. Supplementary materials will be distributed over the course of the semester.


Introductory exercises
1 Microfluidics  
2 Microfabrication  
3 Cells and membranes  
4 Cells and membranes (cont.) Homework 1 due after five days
5 Models of diffusion and cell experiment  
6 Laminar flow Homework 2 due
7 Data analysis using MATLAB®  
8 Research applications Homework 3 due
9 Research paper discussion  
10 Visit research lab Homework 4 due
11 Cell traps  
12 Cell traps (cont.)  
13 Project brainstorming  
14-18 Projects

Homework 5 due Lec #15

Project propsal due Lec #16

19 Device fabrication  
20-23 Projects  

Project presentation

Dry runs

25 Projects  
26 Project presentations   Tell A Friend